Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005715.1 Kokia drynarioides strain JFW-HI SEQ_119944, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25592
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:749 original size:21 final size:20
Alignment explanation
Indices: 723--768 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
713 CTGAACTTCG
* * *
723 AGGTTTGAGGTTCAAAGTTTA
1 AGGTTTAAGATTC-AAGTTCA
744 AGGTTTAAGATTCAAGTTCA
1 AGGTTTAAGATTCAAGTTCA
764 AGGTT
1 AGGTT
769 CGGGTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (20 bp):
AGGTTTAAGATTCAAGTTCA
Found at i:1187 original size:20 final size:19
Alignment explanation
Indices: 1139--1188 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
1129 ACCACATCAG
1139 TAATTTTA-TCA-TGAATT
1 TAATTTTATTCATTGAATT
*
1156 TCAATATT-TTCATTTGAATT
1 T-AATTTTATTCA-TTGAATT
1176 TAATTTTATTCAT
1 TAATTTTATTCAT
1189 AATTTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.31
19 6 0.23
20 11 0.42
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (19 bp):
TAATTTTATTCATTGAATT
Found at i:6088 original size:34 final size:34
Alignment explanation
Indices: 6045--6113 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
6035 TGCATCACTG
6045 TTAGGAGTAATTTATAGGATTTGTATATATTGTT
1 TTAGGAGTAATTTATAGGATTTGTATATATTGTT
*
6079 TTAGGAGTAATTTATGGGATTTGTATATATTGTT
1 TTAGGAGTAATTTATAGGATTTGTATATATTGTT
6113 T
1 T
6114 CCTTATTGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.51
Consensus pattern (34 bp):
TTAGGAGTAATTTATAGGATTTGTATATATTGTT
Found at i:10642 original size:34 final size:34
Alignment explanation
Indices: 10594--10658 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
10584 CGGATGTTAG
10594 GAGTAATTTATGGGATTTGTATATATTGTTTTAT
1 GAGTAATTTATGGGATTTGTATATATTGTTTTAT
*
10628 GAGTAATTTTTGGGATTTGTATATATTGTTT
1 GAGTAATTTATGGGATTTGTATATATTGTTT
10659 CCTTATTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.54
Consensus pattern (34 bp):
GAGTAATTTATGGGATTTGTATATATTGTTTTAT
Found at i:11602 original size:30 final size:30
Alignment explanation
Indices: 11561--11630 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
11551 GTCACCACTA
* * *
11561 ACCACTTTCCGTTATAGA-TGTAACCGAACT
1 ACCATTTTCCGTTACAGACT-TAACCAAACT
11591 ACCATTTTCCGTTACAGACTTAACCAAACT
1 ACCATTTTCCGTTACAGACTTAACCAAACT
11621 ACCATTTTCC
1 ACCATTTTCC
11631 ATCCCCCTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (30 bp):
ACCATTTTCCGTTACAGACTTAACCAAACT
Found at i:13143 original size:20 final size:20
Alignment explanation
Indices: 13118--13162 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
13108 TTTGTTATTT
*
13118 TTTTGA-AAGTTGAGTGACTG
1 TTTTGACAA-TTGAGTAACTG
*
13138 TTTTGACAATTGAGTAATTG
1 TTTTGACAATTGAGTAACTG
13158 TTTTG
1 TTTTG
13163 TCCTCAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.47
Consensus pattern (20 bp):
TTTTGACAATTGAGTAACTG
Found at i:14005 original size:20 final size:19
Alignment explanation
Indices: 13982--14025 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
13972 ATCCATTAGT
13982 TTTAAATAA-TTGTGATTAA
1 TTTAAATAACTT-TGATTAA
*
14001 GTTTAATTAACTTTGATTAA
1 -TTTAAATAACTTTGATTAA
14021 TTTAA
1 TTTAA
14026 GTTAATTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 15 0.68
21 2 0.09
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (19 bp):
TTTAAATAACTTTGATTAA
Found at i:18438 original size:21 final size:21
Alignment explanation
Indices: 18412--18452 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
18402 TTTTAAACTT
18412 ATAAAAT-TTATTTTAATTTTG
1 ATAAAATATT-TTTTAATTTTG
18433 ATAAAATACTTTTTTAATTT
1 ATAAAATA-TTTTTTAATTT
18453 AGTTGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 9 0.50
23 2 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
ATAAAATATTTTTTAATTTTG
Found at i:20677 original size:12 final size:12
Alignment explanation
Indices: 20662--20704 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
20652 GAACATGTTC
20662 ATATGTTCATTT
1 ATATGTTCATTT
**
20674 ATATGTTCATGA
1 ATATGTTCATTT
*
20686 ACATGTTCATTT
1 ATATGTTCATTT
20698 A-ATGTTC
1 ATATGTTC
20705 GTGGATATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.49
Consensus pattern (12 bp):
ATATGTTCATTT
Found at i:20714 original size:23 final size:24
Alignment explanation
Indices: 20662--20716 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
20652 GAACATGTTC
20662 ATATGTTCATTTATATGTTCATGA
1 ATATGTTCATTTATATGTTCATGA
* * *
20686 ACATGTTCATTTA-ATGTTCGTGG
1 ATATGTTCATTTATATGTTCATGA
20709 ATATGTTC
1 ATATGTTC
20717 GGTTATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.47
Consensus pattern (24 bp):
ATATGTTCATTTATATGTTCATGA
Found at i:22837 original size:19 final size:20
Alignment explanation
Indices: 22804--22842 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
22794 TCTCAACAAA
22804 AATTATAAATTAATTCAAAAT
1 AATTATAAA-TAATTCAAAAT
22825 AATTATAAA-AATTCAAAA
1 AATTATAAATAATTCAAAA
22843 ATGTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTATAAATAATTCAAAAT
Found at i:23126 original size:19 final size:20
Alignment explanation
Indices: 23099--23142 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
23089 ATTTTTTTAA
23099 ATTTAACTCGA-ACAATTTC
1 ATTTAACTCGATACAATTTC
* *
23118 ATTTGACTCGATTTCAATTTC
1 ATTTAACTCGA-TACAATTTC
23139 ATTT
1 ATTT
23143 CATTCGACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (20 bp):
ATTTAACTCGATACAATTTC
Done.